You can't connect from a container to the host network. That's probably why rAthena can't connect to MySQL.
Assuming your load balancer is just a debian server, you can follow the steps in the README of the repository I mentioned in earlier posts ignoring the MySQL setup with Docker (since you already have one).
You will need to make a small modification to the `run` command of your server like this:
sudo docker run -it --network host -v 6900:6900 -v 5121:5121 -v 6121:6121 --name=my-running-server my-cool-server
This `--network host` option will allow the Docker container to use the host's network, so you will be able to access your MySQL server, which is outside Docker.
The last part I didn't understand very well. But I think for a generic answer I'll say it depends. You can have all the services (MySQL, Apache, rAthena, etc...) in the same server or split in multiple servers. Moreover, you can have all of them split in multiple containers in the same server. So it depends on what do you want to do.